Contacts of the strand formed by residues 615 - 620 (chain D) in PDB entry 1XMI
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 615 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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447D LYS 4.7 7.1 + - - +
448D ILE* 5.9 3.4 - - + -
452D GLN* 4.8 17.9 + - - +
453D LEU 3.2 3.9 + - - +
454D LEU* 3.3 18.9 - - + +
455D ALA 3.0 22.0 + - - -
613D ALA* 3.4 7.7 - - - +
614D ASP* 1.3 90.2 + - + +
616D ILE* 1.3 64.0 + - - +
627D TYR* 3.7 35.1 + - + +
628D GLY* 3.3 20.2 - - - +
629D THR* 4.3 14.4 - - - +
632D GLU* 5.7 0.4 - - - -
514E GLU* 6.0 1.4 + - - -
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Residues in contact with ILE 616 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454D LEU* 3.8 2.9 - - - -
455D ALA* 3.2 12.3 - - + +
610D LEU* 3.4 48.2 - - + +
613D ALA* 4.1 1.8 - - + +
615D LYS* 1.3 79.3 - - - +
617D LEU* 1.3 59.9 + - - +
618D ILE* 3.8 15.5 - - + -
626D PHE* 3.6 19.5 - - + -
627D TYR* 3.4 8.8 - - - -
628D GLY 2.6 41.0 + - - +
629D THR* 4.1 3.4 - - - -
630D PHE* 4.2 15.3 - - - +
633D LEU* 3.6 31.0 - - + -
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Residues in contact with LEU 617 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444D ILE* 4.7 6.1 - - + -
445D ASN 5.4 2.5 - - - +
446D PHE* 4.2 21.8 - - + -
454D LEU* 4.2 11.0 - - + -
455D ALA 2.7 12.1 + - - +
456D VAL* 3.3 13.2 - - + +
457D ALA 2.9 25.8 + - - +
467D LEU* 3.8 29.2 - - + -
616D ILE* 1.3 75.1 - - - +
618D ILE* 1.3 65.5 + - - +
619D LEU* 3.9 26.9 - - + -
624D SER* 3.5 25.8 - - - +
626D PHE 3.4 7.9 - - - +
627D TYR* 4.5 11.4 - - + -
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Residues in contact with ILE 618 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455D ALA 5.6 0.2 - - - +
457D ALA* 3.4 27.4 - - + +
458D GLY* 4.8 2.5 - - - -
610D LEU* 4.2 4.0 - - + -
616D ILE* 3.8 27.4 - - + -
617D LEU* 1.3 76.0 - - - +
619D LEU* 1.3 61.0 + - - +
624D SER* 3.8 3.1 - - - -
625D TYR* 2.8 52.5 + - + -
626D PHE* 2.8 34.6 + - + +
633D LEU* 4.3 0.7 - - + -
640D PHE* 3.6 36.6 - - + -
643D LYS* 4.2 10.1 - - - -
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Residues in contact with LEU 619 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441D LEU* 4.3 10.3 - - + -
444D ILE* 4.0 20.0 - - + -
456D VAL* 4.0 21.1 - - + -
457D ALA 2.8 14.2 + - - +
458D GLY* 3.5 18.7 - - - -
459D SER* 4.4 1.2 + - - -
462D ALA* 3.6 25.0 - - + +
463D GLY 3.8 29.4 - - - +
464D LYS* 3.9 5.4 - - + +
467D LEU* 4.6 7.2 - - + -
617D LEU* 3.8 29.3 + - + -
618D ILE* 1.3 77.3 - - - +
620D HIS* 1.3 61.7 + - - +
622D GLY 4.8 1.8 - - - -
623D SER 3.4 13.5 - - - +
625D TYR* 4.6 0.4 - - - -
643D LYS* 5.0 2.3 + - - -
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Residues in contact with HIS 620 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459D SER* 5.2 9.0 + - - -
462D ALA* 4.4 0.9 - - - -
618D ILE 4.1 0.4 + - - -
619D LEU* 1.3 73.6 + - - +
621D GLU* 1.3 98.8 + - + +
622D GLY 3.1 0.2 - - - -
623D SER* 2.8 28.5 + - - +
625D TYR* 4.1 24.5 - + + -
643D LYS* 3.9 19.7 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il